Vcf 4.1 to 4.0

Question

[MMK]

Hello!!

I have a VCF file version 4.1 and I want to change it to 4.0 so I can use it in a program (GRAB of family genomics http://familygenomics.systemsbiology.net/grab).

I tried to use vcf-convert but I get the following error:

FIXME: expected indel at 10:85105 at /sw/apps/bioinfo/vcftools/0.1.12/milou/bin/vcf-convert line 21
main::error('FIXME: expected indel at 10:85105\x{a}') called at /sw/apps/bioinfo/vcftools/0.1.12/milou/bin/vcf-convert line 115
main::convert_file('HASH(0x22eed48)') called at /sw/apps/bioinfo/vcftools/0.1.12/milou/bin/vcf-convert line 12

How can I fix it? Any advice? Any other way to solve my problem?

Thank you!

[Eugenie]

Hi, I'm also looking for some 4.1 -> 4.0 converter but seems like vcf-convert only works for versions up to 4.0.

"Convert between VCF versions, currently from VCFv3.3 to VCFv4.0."

Update: it works for 4.1;) did you compress and index your vcf? (bgzip and tabix)

NB: in case you have indels (not only SNPs) you need to give reference sequence:

-r, --refseq <file>              The reference sequence in samtools faindexed fasta file. (Not required with SNPs only.)